Honestly, ATM I don't know where to find a proper documentation on Java 9 and its package rules - feel free to point me at that direction.
But I am quite positive this problem is due to cumbersome modular changes in JDK 9 - if you think about it, default package makes no sense in JDK 9. You can never turn it into a module as those are based on exporting/requiring packages and if you have no package identifier...well, you have no handle for it.

As for the difference in between web app on Tomcat and SE ap, Tomcat can play a significant role there, as it will have separate CL trying to load such class with no package. Or it might have its own classes in default package which might be a source of conflict. But I am just guessing here.

Any thoughts/ideas are welcome